I suspect that the <IRremote.h> library may be utilizing some of the timers that the PWM command uses to control pins 3 & 11.Why don't you just load the example program Fading from the Arduino IDE file menu. Then modify theint ledPin = 9; // LED connected to digital pin 9 line to use pin 3 and then pin 11 and see if the pins work properly. Be sure to use series current limiting resistor with an LED if that is how you are testing for PWM outputs.

I also discovered, through my own stupidity, that tone breaks PWM on pins 3 and 11. I should have read every aspect about tone() before using it but it's so attempting that I grab something and use it without knowing its limitations. So if you do this, it won't work, the pin won't turn on: